Pelagophyceae

RCC

Metabarcodes

Datasets included

All public data sets
dataset_id dataset_code dataset_name gene_region
1 OSD_2014_V4_LGC Ocean Sampling Day - 2014 - V4 LGC V4
2 OSD_2015_V4 Ocean Sampling Day - 2015 - V4 V4
3 OSD_2014_V4_LW Ocean Sampling Day - 2014 - V4 LW V4
5 MALINA_Monier_2014 Arctic Ocean, Beaufort Sea, MALINA cruise - 2009 V4
6 Arctic_Stecher_2016 Central Arctic Ocean - 2012 V4
9 Nansen_Metfies_2016 Nansen Basin - 2012 V4
11 Fieldes_Bay_Luo_2016 Fieldes Bay, Antarctic - 2013 V4
19 Baltic_Sea_2012_2013 Gulf of Finland - 2012-2013 V4
20 Oslo_fjord_2009_2011 Oslo fjord - 2009-2011 V4
33 Tsunami_18S Tsunami deposits 18S R1 V4
34 Malaspina_vertical_V4 Malaspina expedition - vertical profiles - 2010-2011 V4
35 Malaspina_surface_V4 Malaspina expedition - surface - 2010-2011 V4
36 Blanes_2004_2013 Blanes Time Series - 2004-2013 V4
37 Baffin_Bay_Joli_2013 Baffin Bay - 2013 V4
38 White_Sea_2013_2015 White Sea - 2013-2015 V4
39 Arctic_Ocean_PS80_2012 Arctic Ocean - Polarstern expedition ARK-XXVII/3 - 2012 V4
40 Arctic_Ocean_Survey Arctic Ocean Survey - 2005-2011 V4
41 Chukchi_Sea_ICESCAPE Chukchi Sea - ICESCAPE - 2010 V4
42 Arctic_Nares_Strait Nares Strait - 2014 V4
43 Baltic_Gdansk_2012 Gdansk Gulf - 2012 V4
44 Baltic_Gdansk_2012_Hapto Gdansk Gulf - 2012 Hapto V4
49 Naples_2011 Bay of Naples - 2011 V4
15 Tara_Oceans Tara Oceans - 2009-2012 V9
Data sets selected
dataset_id dataset_code dataset_name gene_region
1 OSD_2014_V4_LGC Ocean Sampling Day - 2014 - V4 LGC V4
2 OSD_2015_V4 Ocean Sampling Day - 2015 - V4 V4
34 Malaspina_vertical_V4 Malaspina expedition - vertical profiles - 2010-2011 V4
35 Malaspina_surface_V4 Malaspina expedition - surface - 2010-2011 V4
36 Blanes_2004_2013 Blanes Time Series - 2004-2013 V4
15 Tara_Oceans Tara Oceans - 2009-2012 V9

Summarize function

  • At species level
summarise_asv_set <- function(one_asv_set, directory) {
  
  # one_asv_set <- filter(asv_set[["V4"]]$df, dataset_id != 36)
  # directory = "../metabarcodes/V4/"
  
  summary_species <- phyloseq_long_treemap(one_asv_set, genus, species, "Species" )

  
# Normalize by total number of Pelagophyceae reads
  asv_class <- one_asv_set %>% 
    group_by(file_code) %>% 
    summarise(reads_class = sum(n_reads)) 
  
  one_asv_set <- left_join(one_asv_set, asv_class) %>% 
    mutate (pct_class = n_reads/reads_class*100,
            pct_total = n_reads/reads_total*100)
  
  summary_pct <- one_asv_set %>% 
    group_by(species) %>% 
    summarise(pct_class = mean(pct_class, na.rm = TRUE),
              pct_total = mean(pct_total, na.rm = TRUE))
  
  summary_species <- left_join(summary_species$df, summary_pct)
  print(knitr::kable(summary_species))
  
  openxlsx::write.xlsx(summary_species, str_c(directory, "summary_species.xlsx"))

#     
# # Map of number of samples where genus found   
#   asv_summary <- one_asv_set %>% 
#       distinct(file_code, genus, longitude, latitude, .keep_all = TRUE) %>% 
#       count(genus, species, longitude, latitude, name="n_samples") 
#     
# #   print(knitr::kable(asv_summary))
    

  world <- map_data("world")

  g <- ggplot() + 
    geom_polygon(data = world, aes(x=long, y = lat, group = group), fill="grey") + 
    coord_fixed(1.3) +
    geom_point(data=one_asv_set, aes(x=longitude, y=latitude, size=pct_class), fill="blue", shape=21) + 
    # scale_size_area(trans="log10") +
    ggtitle("Percent of Pelagophyceae") +
    facet_wrap(vars(species))
  print(g)
  
  for (one_species in unique(one_asv_set$species)) {
    df <- one_asv_set %>% 
      filter(species == one_species) %>% 
      select(longitude, latitude, pct_class) %>% 
      rename(z=pct_class)
    gg <- map_distribution(df, map_title = str_c(one_species," - % of Pelagophyceae"))
    print(gg)
    ggsave(plot= gg , filename=str_c(directory,"maps_pct_pelago/map_",one_species,"_pct_pelago.pdf"),
       width = 15 , height = 12, scale=1.80, 
       units="cm", useDingbats=FALSE)
  }
  
  for (one_species in unique(one_asv_set$species)) {
    df <- one_asv_set %>% 
      filter(species == one_species) %>% 
      select(longitude, latitude, pct_total) %>% 
      rename(z=pct_total)
    gg <- map_distribution(df, map_title = str_c(one_species," - % of Total reads"),
                           z_limits = c(0, 50),
                           z_breaks = c(5, 10, 20, 40, 50))
    print(gg)
    ggsave(plot= gg , filename=str_c(directory,"maps_pct_total/map_",one_species,"_pct_total.pdf"),
       width = 15 , height = 12, scale=1.80, 
       units="cm", useDingbats=FALSE)
  }


  return(TRUE)
   
    
  }

Get the data

Joining, by = "file_code"
Joining, by = "species"



genus                      species                         n_reads    pct_class   pct_total
-------------------------  -----------------------------  --------  -----------  ----------
Ankylochrysis              Ankylochrysis_lutea                 833   67.5159512   0.4905626
Ankylochrysis              Ankylochrysis_sp.                   104   55.0653595   0.0404306
Aureococcus                Aureococcus_anophagefferens       25736   27.6070076   0.2275524
Aureoumbra                 Aureoumbra_lagunensis                50   36.1818525   0.0583039
Chrysocystis               Chrysocystis_fragilis              1172   26.5399034   0.1376429
Chrysoreinhardia           Chrysoreinhardia_sp.                  2    0.0042324   0.0020712
Pelagococcus               Pelagococcus_sp.                   5418   23.0231659   0.0699292
Pelagococcus               Pelagococcus_subviridis               1    0.1996008   0.0010934
Pelagomonadaceae_clade_A   Pelagomonadaceae_clade_A_sp.      17688   26.6221946   0.1094061
Pelagomonadaceae_X         Pelagomonadaceae_X_sp.              286    1.6478726   0.0124078
Pelagomonas                Pelagomonas_calceolata           614671   53.3934368   2.1871642
Pelagophyceae_Svalbard     Pelagophyceae_Svalbard_sp.          498   59.8075003   0.3833255
Pelagophyceae_XXX          Pelagophyceae_XXX_sp.             21150   20.6051618   0.1155214
Sarcinochrysidaceae_X      Sarcinochrysidaceae_X_sp.           566   46.5579201   0.0752083
Sarcinochrysis             Sarcinochrysis_sp.                 3056   45.9810724   0.1722144
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Joining, by = "species"



genus                      species                         n_reads   pct_class   pct_total
-------------------------  -----------------------------  --------  ----------  ----------
Aureococcus                Aureococcus_anophagefferens      887561   22.788344   0.1125895
Pelagococcus               Pelagococcus_sp.                  25784    6.688237   0.0075565
Pelagomonadaceae_clade_A   Pelagomonadaceae_clade_A_sp.      16250    7.147905   0.0029203
Pelagomonadaceae_X         Pelagomonadaceae_X_sp.            18632    4.343436   0.0028249
Pelagomonas                Pelagomonas_calceolata          3210461   72.359834   0.3401518
Sarcinochrysidaceae_X      Sarcinochrysidaceae_X_sp.           473    4.335542   0.0011510
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2020-05-05